SequestOutfile

class pyopenms.SequestOutfile

Bases: object

Cython implementation of _SequestOutfile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SequestOutfile.html

Representation of a Sequest output file

__init__()

  • Cython signature: void SequestOutfile() Representation of a Sequest output file

  • Cython signature: void SequestOutfile(SequestOutfile &)

Methods

__init__

  • Cython signature: void SequestOutfile()

getACAndACType

Cython signature: void getACAndACType(String line, String & accession, String & accession_type) Retrieves the accession type and accession number from a protein description line

getColumns

Cython signature: bool getColumns(const String & line, libcpp_vector[String] & substrings, size_t number_of_columns, size_t reference_column) Retrieves columns from a Sequest outfile line

getSequences

load

Cython signature: void load(const String & result_filename, libcpp_vector[PeptideIdentification] & peptide_identifications, ProteinIdentification & protein_identification, double p_value_threshold, libcpp_vector[double] & pvalues, const String & database, bool ignore_proteins_per_peptide)
getACAndACType()

Cython signature: void getACAndACType(String line, String & accession, String & accession_type) Retrieves the accession type and accession number from a protein description line

getColumns()

Cython signature: bool getColumns(const String & line, libcpp_vector[String] & substrings, size_t number_of_columns, size_t reference_column) Retrieves columns from a Sequest outfile line

getSequences()
load()

Cython signature: void load(const String & result_filename, libcpp_vector[PeptideIdentification] & peptide_identifications, ProteinIdentification & protein_identification, double p_value_threshold, libcpp_vector[double] & pvalues, const String & database, bool ignore_proteins_per_peptide)

Parameters

  • result_filename – The file to be loaded

  • peptide_identifications – The identifications

  • protein_identification – The protein identifications

  • p_value_threshold – The significance level (for the peptide hit scores)

  • pvalues – A list with the pvalues of the peptides (pvalues computed with peptide prophet)

  • database – The database used for the search

  • ignore_proteins_per_peptide – This is a hack to deal with files that use a suffix like “+1” in column “Reference”, but do not actually list extra protein references in subsequent lines